Sliding Restriction

Helicase enzymes access the genetic information stored in double-helical DNA and RNA by opening the individual strands. Pseudo-helicases, including bacterial Type III restriction enzymes, use adenosine triphosphate (ATP) hydrolysis to communicate between two distant restriction sites on the same DNA and excise it only if the DNA is sensed as “foreign.” Schwarz et al. (p. 353) show that the bacterial Type III restriction enzyme, EcoP15I, undergoes an ATP-dependent conformational switch that promotes sliding along the DNA to allow the enzyme to localize to its target.

Abstract

Helicases are ubiquitous adenosine triphosphatases (ATPases) with widespread roles in genome metabolism. Here, we report a previously undescribed functionality for ATPases with helicase-like domains; namely, that ATP hydrolysis can trigger ATP-independent long-range protein diffusion on DNA in one dimension (1D). Specifically, using single-molecule fluorescence microscopy we show that the Type III restriction enzyme EcoP15I uses its ATPase to switch into a distinct structural state that diffuses on DNA over long distances and long times. The switching occurs only upon binding to the target site and requires hydrolysis of ~30 ATPs. We define the mechanism for these enzymes and show how ATPase activity is involved in DNA target site verification and 1D signaling, roles that are common in DNA metabolism: for example, in nucleotide excision and mismatch repair.